replace grobid2json with grobid_tei_xml

This first iteration uses the .to_legacy_dict() helpers for backwards
compatibility

5 files changed, 21 insertions, 252 deletions

diff --git a/fatcat_scholar/grobid2json.py b/fatcat_scholar/grobid2json.py
deleted file mode 100755
index c99b9ed..0000000
--- a/fatcat_scholar/grobid2json.py
+++ /dev/null
@@ -1,236 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-NB: adapted to work as a library for PDF extraction. Will probably be
-re-written eventually to be correct, complete, and robust; this is just a
-first iteration.
-
-This script tries to extract everything from a GROBID TEI XML fulltext dump:
-
-- header metadata
-- affiliations
-- references (with context)
-- abstract
-- fulltext
-- tables, figures, equations
-
-A flag can be specified to disable copyright encumbered bits (--no-emcumbered):
-
-- abstract
-- fulltext
-- tables, figures, equations
-
-Prints JSON to stdout, errors to stderr
-
-This file copied from the sandcrawler repository.
-"""
-
-import argparse
-import io
-import json
-import xml.etree.ElementTree as ET
-from typing import Any, AnyStr, Dict, List, Optional
-
-xml_ns = "http://www.w3.org/XML/1998/namespace"
-ns = "http://www.tei-c.org/ns/1.0"
-
-
-def all_authors(elem: Optional[ET.Element], ns: str = ns) -> List[Dict[str, Any]]:
-    if not elem:
-        return []
-    names = []
-    for author in elem.findall(".//{%s}author" % ns):
-        pn = author.find("./{%s}persName" % ns)
-        if not pn:
-            continue
-        given_name = pn.findtext("./{%s}forename" % ns) or None
-        surname = pn.findtext("./{%s}surname" % ns) or None
-        full_name = " ".join(pn.itertext())
-        obj: Dict[str, Any] = dict(name=full_name)
-        if given_name:
-            obj["given_name"] = given_name
-        if surname:
-            obj["surname"] = surname
-        ae = author.find("./{%s}affiliation" % ns)
-        if ae:
-            affiliation: Dict[str, Any] = dict()
-            for on in ae.findall("./{%s}orgName" % ns):
-                on_type = on.get("type")
-                if on_type:
-                    affiliation[on_type] = on.text
-            addr_e = ae.find("./{%s}address" % ns)
-            if addr_e:
-                address = dict()
-                for t in addr_e.getchildren():
-                    address[t.tag.split("}")[-1]] = t.text
-                if address:
-                    affiliation["address"] = address
-                # affiliation['address'] = {
-                #    'post_code': addr.findtext('./{%s}postCode' % ns) or None,
-                #    'settlement': addr.findtext('./{%s}settlement' % ns) or None,
-                #    'country': addr.findtext('./{%s}country' % ns) or None,
-                # }
-            obj["affiliation"] = affiliation
-        names.append(obj)
-    return names
-
-
-def journal_info(elem: ET.Element) -> Dict[str, Any]:
-    journal = dict()
-    journal["name"] = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
-    journal["publisher"] = elem.findtext(
-        f".//{{{ns}}}publicationStmt/{{{ns}}}publisher"
-    )
-    if journal["publisher"] == "":
-        journal["publisher"] = None
-    journal["issn"] = elem.findtext('.//{%s}idno[@type="ISSN"]' % ns)
-    journal["eissn"] = elem.findtext('.//{%s}idno[@type="eISSN"]' % ns)
-    journal["volume"] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
-    journal["issue"] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
-    keys = list(journal.keys())
-
-    # remove empty/null keys
-    for k in keys:
-        if not journal[k]:
-            journal.pop(k)
-    return journal
-
-
-def biblio_info(elem: ET.Element, ns: str = ns) -> Dict[str, Any]:
-    ref: Dict[str, Any] = dict()
-    ref["id"] = elem.attrib.get("{http://www.w3.org/XML/1998/namespace}id")
-    ref["unstructured"] = elem.findtext('.//{%s}note[@type="raw_reference"]' % ns)
-    # Title stuff is messy in references...
-    ref["title"] = elem.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
-    other_title = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
-    if other_title:
-        if ref["title"]:
-            ref["journal"] = other_title
-        else:
-            ref["journal"] = None
-            ref["title"] = other_title
-    ref["authors"] = all_authors(elem, ns=ns)
-    ref["publisher"] = elem.findtext(f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
-    if not ref["publisher"]:
-        ref["publisher"] = elem.findtext(f".//{{{ns}}}imprint/{{{ns}}}publisher")
-    if ref["publisher"] == "":
-        ref["publisher"] = None
-    date = elem.find('.//{%s}date[@type="published"]' % ns)
-    ref["date"] = (date is not None) and date.attrib.get("when")
-    ref["volume"] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
-    ref["issue"] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
-    ref["doi"] = elem.findtext('.//{%s}idno[@type="DOI"]' % ns)
-    ref["arxiv_id"] = elem.findtext('.//{%s}idno[@type="arXiv"]' % ns)
-    if ref["arxiv_id"] and ref["arxiv_id"].startswith("arXiv:"):
-        ref["arxiv_id"] = ref["arxiv_id"][6:]
-    ref["pmcid"] = elem.findtext('.//{%s}idno[@type="PMCID"]' % ns)
-    ref["pmid"] = elem.findtext('.//{%s}idno[@type="PMID"]' % ns)
-    el = elem.find('.//{%s}biblScope[@unit="page"]' % ns)
-    if el is not None:
-        if el.attrib.get("from") and el.attrib.get("to"):
-            ref["pages"] = "{}-{}".format(el.attrib["from"], el.attrib["to"])
-        else:
-            ref["pages"] = el.text
-    el = elem.find(".//{%s}ptr[@target]" % ns)
-    if el is not None:
-        ref["url"] = el.attrib["target"]
-        # Hand correction
-        if ref["url"].endswith(".Lastaccessed"):
-            ref["url"] = ref["url"].replace(".Lastaccessed", "")
-        if ref["url"].startswith("<"):
-            ref["url"] = ref["url"][1:]
-        if ">" in ref["url"]:
-            ref["url"] = ref["url"].split(">")[0]
-    else:
-        ref["url"] = None
-    return ref
-
-
-def teixml2json(content: AnyStr, encumbered: bool = True) -> Dict[str, Any]:
-
-    if isinstance(content, str):
-        tree = ET.parse(io.StringIO(content))
-    elif isinstance(content, bytes):
-        tree = ET.parse(io.BytesIO(content))
-
-    info: Dict[str, Any] = dict()
-
-    # print(content)
-    # print(content.getvalue())
-    tei = tree.getroot()
-
-    header = tei.find(".//{%s}teiHeader" % ns)
-    if header is None:
-        raise ValueError("XML does not look like TEI format")
-    application_tag = header.findall(f".//{{{ns}}}appInfo/{{{ns}}}application")[0]
-    info["grobid_version"] = application_tag.attrib["version"].strip()
-    info["grobid_timestamp"] = application_tag.attrib["when"].strip()
-    info["title"] = header.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
-    info["authors"] = all_authors(
-        header.find(f".//{{{ns}}}sourceDesc/{{{ns}}}biblStruct")
-    )
-    info["journal"] = journal_info(header)
-    date = header.find('.//{%s}date[@type="published"]' % ns)
-    info["date"] = (date is not None) and date.attrib.get("when")
-    info["fatcat_release"] = header.findtext('.//{%s}idno[@type="fatcat"]' % ns)
-    info["doi"] = header.findtext('.//{%s}idno[@type="DOI"]' % ns)
-    if info["doi"]:
-        info["doi"] = info["doi"].lower()
-
-    refs = []
-    for (i, bs) in enumerate(tei.findall(f".//{{{ns}}}listBibl/{{{ns}}}biblStruct")):
-        ref = biblio_info(bs)
-        ref["index"] = i
-        refs.append(ref)
-    info["citations"] = refs
-
-    text = tei.find(".//{%s}text" % (ns))
-    # print(text.attrib)
-    if text and text.attrib.get("{%s}lang" % xml_ns):
-        info["language_code"] = text.attrib["{%s}lang" % xml_ns]  # xml:lang
-
-    if encumbered:
-        el = tei.find(f".//{{{ns}}}profileDesc/{{{ns}}}abstract")
-        info["abstract"] = (el or None) and " ".join(el.itertext()).strip()
-        el = tei.find(f".//{{{ns}}}text/{{{ns}}}body")
-        info["body"] = (el or None) and " ".join(el.itertext()).strip()
-        el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="acknowledgement"]')
-        info["acknowledgement"] = (el or None) and " ".join(el.itertext()).strip()
-        el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="annex"]')
-        info["annex"] = (el or None) and " ".join(el.itertext()).strip()
-
-    # remove empty/null keys
-    keys = list(info.keys())
-    for k in keys:
-        if not info[k]:
-            info.pop(k)
-    return info
-
-
-def main() -> None:  # pragma no cover
-    parser = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        description="GROBID TEI XML to JSON",
-        usage="%(prog)s [options] <teifile>...",
-    )
-    parser.add_argument(
-        "--no-encumbered",
-        action="store_true",
-        help="don't include ambiguously copyright encumbered fields (eg, abstract, body)",
-    )
-    parser.add_argument("teifiles", nargs="+")
-
-    args = parser.parse_args()
-
-    for filename in args.teifiles:
-        content = open(filename, "r").read()
-        print(
-            json.dumps(
-                teixml2json(content, encumbered=(not args.no_encumbered)),
-                sort_keys=True,
-            )
-        )
-
-
-if __name__ == "__main__":  # pragma no cover
-    main()
diff --git a/fatcat_scholar/query_citation.py b/fatcat_scholar/query_citation.py
index 6cc9086..dea4f02 100644
--- a/fatcat_scholar/query_citation.py
+++ b/fatcat_scholar/query_citation.py
@@ -10,9 +10,7 @@ timeout and try/except! In the future, perhaps should be async so it can run in
 parallel with "regular" query?
 """
 
-import io
 import sys
-import xml.etree.ElementTree as ET
 from typing import Any, Optional, Tuple
 
 import fuzzycat.common
@@ -20,9 +18,9 @@ import fuzzycat.verify
 import requests
 from fatcat_openapi_client import ReleaseContrib, ReleaseEntity, ReleaseExtIds
 from fuzzycat.matching import match_release_fuzzy
+from grobid_tei_xml import parse_citations_xml
 
 from fatcat_scholar.api_entities import entity_to_dict
-from fatcat_scholar.grobid2json import biblio_info
 
 
 def grobid_process_citation(
@@ -47,11 +45,10 @@ def grobid_process_citation(
 
 
 def transform_grobid(raw_xml: str) -> Optional[dict]:
-    # first, remove any xmlns stuff
-    raw_xml = raw_xml.replace('xmlns="http://www.tei-c.org/ns/1.0"', "")
-    tree = ET.parse(io.StringIO(raw_xml))
-    root = tree.getroot()
-    ref = biblio_info(root, ns="")
+    ref_list = parse_citations_xml(raw_xml)
+    if not ref_list:
+        return None
+    ref = ref_list[0]
     if not any(ref.values()):
         return None
     return ref
diff --git a/fatcat_scholar/transform.py b/fatcat_scholar/transform.py
index f805e7b..caeff21 100644
--- a/fatcat_scholar/transform.py
+++ b/fatcat_scholar/transform.py
@@ -8,9 +8,9 @@ from typing import Any, Dict, List, Optional, Sequence
 
 import sentry_sdk
 from fatcat_openapi_client import FileEntity, ReleaseEntity, WebcaptureEntity
+from grobid_tei_xml import parse_document_xml
 
 from fatcat_scholar.config import GIT_REVISION, settings
-from fatcat_scholar.grobid2json import teixml2json
 from fatcat_scholar.identifiers import clean_doi, clean_pmcid
 from fatcat_scholar.schema import (
     AccessType,
@@ -521,7 +521,8 @@ def transform_heavy(heavy: IntermediateBundle) -> Optional[ScholarDoc]:
             if f.ident == heavy.grobid_fulltext["file_ident"]
         ][0]
         try:
-            tei_dict: Optional[dict] = teixml2json(heavy.grobid_fulltext["tei_xml"])
+            tei_doc = parse_document_xml(heavy.grobid_fulltext["tei_xml"])
+            tei_dict = tei_doc.to_legacy_dict()
         except xml.etree.ElementTree.ParseError:
             tei_dict = None
         if tei_dict:
@@ -900,7 +901,8 @@ def refs_from_heavy(heavy: IntermediateBundle) -> Sequence[RefStructured]:
             for r in heavy.releases
             if r.ident == heavy.grobid_fulltext["release_ident"]
         ][0]
-        tei_dict = teixml2json(heavy.grobid_fulltext["tei_xml"])
+        tei_doc = parse_document_xml(heavy.grobid_fulltext["tei_xml"])
+        tei_dict = tei_doc.to_legacy_dict()
         fulltext_refs = refs_from_grobid(fulltext_release, tei_dict)
 
     crossref_refs: List[RefStructured] = []
diff --git a/tests/test_grobid2json.py b/tests/test_grobid2json.py
index 345fd91..adf36a1 100644
--- a/tests/test_grobid2json.py
+++ b/tests/test_grobid2json.py
@@ -1,12 +1,17 @@
-from fatcat_scholar.grobid2json import teixml2json
+from grobid_tei_xml import parse_document_xml
 
 
-def test_grobid_teixml2json() -> None:
+def test_grobid_parse() -> None:
+    """
+    This function formerly tested the grobid2json file in this project. Now it
+    tests backwards-compatibility of the grobid_tei_xml library.
+    """
 
     with open("tests/files/example_grobid.tei.xml", "r") as f:
         blob = f.read()
 
-    obj = teixml2json(blob, True)
+    doc = parse_document_xml(blob)
+    obj = doc.to_legacy_dict()
 
     assert (
         obj["title"]
diff --git a/tests/test_refs_transform.py b/tests/test_refs_transform.py
index 5f15adf..2fc210f 100644
--- a/tests/test_refs_transform.py
+++ b/tests/test_refs_transform.py
@@ -1,8 +1,8 @@
 import json
 
 from fatcat_openapi_client import ReleaseEntity
+from grobid_tei_xml import parse_document_xml
 
-from fatcat_scholar.grobid2json import teixml2json
 from fatcat_scholar.transform import refs_from_crossref, refs_from_grobid
 
 
@@ -19,7 +19,8 @@ def test_transform_refs_grobid() -> None:
         ext_ids={},
     )
 
-    tei_dict = teixml2json(blob, True)
+    tei_doc = parse_document_xml(blob)
+    tei_dict = tei_doc.to_legacy_dict()
     refs = refs_from_grobid(dummy_release, tei_dict)
 
     ref = refs[12]